Hierarchy For All Packages

Package Hierarchies:

• de.charite.compbio.jannovar,
• de.charite.compbio.jannovar.annotation,
• de.charite.compbio.jannovar.annotation.builders,
• de.charite.compbio.jannovar.data,
• de.charite.compbio.jannovar.datasource,
• de.charite.compbio.jannovar.hgnc,
• de.charite.compbio.jannovar.impl.intervals,
• de.charite.compbio.jannovar.impl.parse,
• de.charite.compbio.jannovar.impl.parse.ensembl,
• de.charite.compbio.jannovar.impl.parse.flatbed,
• de.charite.compbio.jannovar.impl.parse.gtfgff,
• de.charite.compbio.jannovar.impl.parse.refseq,
• de.charite.compbio.jannovar.impl.parse.ucsc,
• de.charite.compbio.jannovar.impl.util,
• de.charite.compbio.jannovar.mendel,
• de.charite.compbio.jannovar.mendel.impl,
• de.charite.compbio.jannovar.pedigree,
• de.charite.compbio.jannovar.reference

Class Hierarchy

• java.lang.Object
  • de.charite.compbio.jannovar.mendel.impl.AbstractMendelianChecker
    • de.charite.compbio.jannovar.mendel.impl.MendelianCheckerAD
    • de.charite.compbio.jannovar.mendel.impl.MendelianCheckerAR
    • de.charite.compbio.jannovar.mendel.impl.MendelianCheckerARCompoundHet
    • de.charite.compbio.jannovar.mendel.impl.MendelianCheckerARHom
    • de.charite.compbio.jannovar.mendel.impl.MendelianCheckerXD
    • de.charite.compbio.jannovar.mendel.impl.MendelianCheckerXR
    • de.charite.compbio.jannovar.mendel.impl.MendelianCheckerXRCompoundHet
    • de.charite.compbio.jannovar.mendel.impl.MendelianCheckerXRHom
  • de.charite.compbio.jannovar.reference.AminoAcidChange
  • de.charite.compbio.jannovar.reference.AminoAcidChangeNormalizer
  • de.charite.compbio.jannovar.annotation.Annotation (implements java.lang.Comparable<T>, de.charite.compbio.jannovar.reference.VariantDescription)
  • de.charite.compbio.jannovar.annotation.builders.AnnotationBuilderDispatcher
  • de.charite.compbio.jannovar.annotation.builders.AnnotationBuilderOptions
  • de.charite.compbio.jannovar.annotation.AnnotationLocation
  • de.charite.compbio.jannovar.annotation.AnnotationLocationBuilder
  • de.charite.compbio.jannovar.annotation.builders.BlockSubstitutionAnnotationBuilder
  • de.charite.compbio.jannovar.reference.CDSInterval
  • de.charite.compbio.jannovar.reference.CDSPosition
  • de.charite.compbio.jannovar.data.Chromosome (implements java.io.Serializable)
  • de.charite.compbio.jannovar.datasource.DataSource
    • de.charite.compbio.jannovar.datasource.FlatBEDDataSource
  • de.charite.compbio.jannovar.datasource.DataSourceFactory
  • de.charite.compbio.jannovar.datasource.DatasourceOptions
  • de.charite.compbio.jannovar.annotation.builders.DeletionAnnotationBuilder
  • de.charite.compbio.jannovar.impl.util.DNAUtils
  • de.charite.compbio.jannovar.reference.DuplicationChecker
  • de.charite.compbio.jannovar.impl.parse.ensembl.EnsemblParser (implements de.charite.compbio.jannovar.impl.parse.TranscriptParser)
  • de.charite.compbio.jannovar.impl.parse.FASTAParser
  • de.charite.compbio.jannovar.impl.parse.FASTARecord
  • de.charite.compbio.jannovar.impl.parse.gtfgff.FeatureRecord (implements java.lang.Comparable<T>)
  • de.charite.compbio.jannovar.impl.parse.gtfgff.FeatureRecordParser
    • de.charite.compbio.jannovar.impl.parse.gtfgff.GFFRecordParser
    • de.charite.compbio.jannovar.impl.parse.gtfgff.GTFRecordParser
  • de.charite.compbio.jannovar.impl.parse.flatbed.FlatBEDFastaParser
  • de.charite.compbio.jannovar.impl.parse.flatbed.FlatBEDParser (implements de.charite.compbio.jannovar.impl.parse.TranscriptParser)
  • de.charite.compbio.jannovar.reference.GenomeInterval (implements java.lang.Comparable<T>, java.io.Serializable)
  • de.charite.compbio.jannovar.reference.GenomePosition (implements java.lang.Comparable<T>, java.io.Serializable)
  • de.charite.compbio.jannovar.reference.GenomeVariant (implements de.charite.compbio.jannovar.reference.VariantDescription)
  • de.charite.compbio.jannovar.reference.GenomeVariantNormalizer
  • de.charite.compbio.jannovar.annotation.builders.GenomicNucleotideChangeBuilder
  • de.charite.compbio.jannovar.mendel.Genotype
  • de.charite.compbio.jannovar.mendel.GenotypeBuilder
  • de.charite.compbio.jannovar.mendel.GenotypeCalls (implements java.lang.Iterable<T>)
  • de.charite.compbio.jannovar.mendel.GenotypeCallsBuilder
  • de.charite.compbio.jannovar.pedigree.GenotypeList
  • de.charite.compbio.jannovar.pedigree.GenotypeListBuilder
  • de.charite.compbio.jannovar.impl.parse.gtfgff.GFFParser
  • de.charite.compbio.jannovar.reference.HG19RefDictBuilder
  • de.charite.compbio.jannovar.hgnc.HGNCParser
  • de.charite.compbio.jannovar.hgnc.HGNCRecord
  • de.charite.compbio.jannovar.annotation.builders.InsertionAnnotationBuilder
  • de.charite.compbio.jannovar.impl.intervals.Interval<T> (implements java.lang.Comparable<T>, java.io.Serializable)
  • de.charite.compbio.jannovar.impl.intervals.IntervalArray<T> (implements java.io.Serializable)
  • de.charite.compbio.jannovar.impl.intervals.IntervalArray.QueryResult
  • de.charite.compbio.jannovar.data.JannovarData (implements java.io.Serializable)
  • de.charite.compbio.jannovar.datasource.JannovarDataFactory
    • de.charite.compbio.jannovar.datasource.FlatBEDJannovarDataFactory
  • de.charite.compbio.jannovar.data.JannovarDataSerializer
  • de.charite.compbio.jannovar.mendel.MendelianInheritanceChecker
  • de.charite.compbio.jannovar.impl.intervals.MutableInterval<T> (implements java.lang.Comparable<T>, java.io.Serializable)
  • de.charite.compbio.jannovar.reference.NucleotidePointLocationBuilder
  • de.charite.compbio.jannovar.impl.util.PathUtil
  • de.charite.compbio.jannovar.pedigree.PedFileContents
  • de.charite.compbio.jannovar.pedigree.PedFileReader
  • de.charite.compbio.jannovar.pedigree.PedFileWriter
  • de.charite.compbio.jannovar.pedigree.Pedigree
  • de.charite.compbio.jannovar.pedigree.Pedigree.IndexedPerson
  • de.charite.compbio.jannovar.pedigree.PedigreeExtractor
  • de.charite.compbio.jannovar.pedigree.PedigreeQueryDecorator
  • de.charite.compbio.jannovar.pedigree.PedPerson
  • de.charite.compbio.jannovar.pedigree.Person
  • de.charite.compbio.jannovar.impl.util.ProgressBar
  • de.charite.compbio.jannovar.data.ReferenceDictionary (implements java.io.Serializable)
  • de.charite.compbio.jannovar.data.ReferenceDictionaryBuilder
  • de.charite.compbio.jannovar.impl.parse.ReferenceDictParser
  • de.charite.compbio.jannovar.impl.parse.refseq.RefSeqParser (implements de.charite.compbio.jannovar.impl.parse.TranscriptParser)
  • de.charite.compbio.jannovar.annotation.builders.SNVAnnotationBuilder
  • de.charite.compbio.jannovar.impl.util.StringUtil
  • de.charite.compbio.jannovar.annotation.builders.StructuralVariantAnnotationBuilder
  • java.lang.Throwable (implements java.io.Serializable)
    • java.lang.Exception
      • java.io.IOException
        • de.charite.compbio.jannovar.impl.parse.InvalidAttributeException
      • de.charite.compbio.jannovar.JannovarException
        • de.charite.compbio.jannovar.annotation.AnnotationException
          • de.charite.compbio.jannovar.annotation.InvalidGenomeVariant
        • de.charite.compbio.jannovar.datasource.FileDownloadException
        • de.charite.compbio.jannovar.mendel.IncompatiblePedigreeException
        • de.charite.compbio.jannovar.reference.InvalidCodonException
        • de.charite.compbio.jannovar.datasource.InvalidDataSourceException
        • de.charite.compbio.jannovar.pedigree.PedParseException
        • de.charite.compbio.jannovar.reference.ProjectionException
        • de.charite.compbio.jannovar.data.SerializationException
        • de.charite.compbio.jannovar.impl.parse.TranscriptParseException
      • java.lang.RuntimeException
        • de.charite.compbio.jannovar.reference.InvalidCoordinateException
        • de.charite.compbio.jannovar.UncheckedJannovarException
  • de.charite.compbio.jannovar.reference.TranscriptInterval
  • de.charite.compbio.jannovar.reference.TranscriptIntervalEndExtractor (implements de.charite.compbio.jannovar.impl.intervals.IntervalEndExtractor<T>)
  • de.charite.compbio.jannovar.reference.TranscriptModel (implements java.lang.Comparable<T>, java.io.Serializable)
  • de.charite.compbio.jannovar.reference.TranscriptModelBuilder
  • de.charite.compbio.jannovar.datasource.TranscriptModelBuilderHGNCExtender
  • de.charite.compbio.jannovar.reference.TranscriptPosition
  • de.charite.compbio.jannovar.reference.TranscriptProjectionDecorator
  • de.charite.compbio.jannovar.reference.TranscriptSequenceChangeHelper
  • de.charite.compbio.jannovar.reference.TranscriptSequenceDecorator
  • de.charite.compbio.jannovar.reference.TranscriptSequenceOntologyDecorator
  • de.charite.compbio.jannovar.impl.parse.TranscriptSupportLevelsSetterFromLengths
  • de.charite.compbio.jannovar.impl.util.Translator
  • de.charite.compbio.jannovar.impl.parse.ucsc.UCSCParser (implements de.charite.compbio.jannovar.impl.parse.TranscriptParser)
  • de.charite.compbio.jannovar.annotation.VariantAnnotations (implements de.charite.compbio.jannovar.reference.VariantDescription)
  • de.charite.compbio.jannovar.annotation.VariantAnnotationsContentDecorator
  • de.charite.compbio.jannovar.annotation.VariantAnnotationsTextGenerator
    • de.charite.compbio.jannovar.annotation.AllAnnotationListTextGenerator
    • de.charite.compbio.jannovar.annotation.BestAnnotationListTextGenerator
  • de.charite.compbio.jannovar.annotation.VariantAnnotator

Interface Hierarchy

• de.charite.compbio.jannovar.impl.intervals.IntervalEndExtractor<T>
• de.charite.compbio.jannovar.impl.parse.TranscriptParser
• de.charite.compbio.jannovar.reference.TranscriptSupportLevels
• de.charite.compbio.jannovar.reference.VariantDescription

Annotation Type Hierarchy

• de.charite.compbio.jannovar.Immutable (implements java.lang.annotation.Annotation)

Enum Hierarchy

• java.lang.Object
  • java.lang.Enum<E> (implements java.lang.Comparable<T>, java.io.Serializable)
    • de.charite.compbio.jannovar.mendel.ModeOfInheritance
    • de.charite.compbio.jannovar.mendel.ChromosomeType
    • de.charite.compbio.jannovar.impl.parse.gtfgff.GFFParser.GFFVersion
    • de.charite.compbio.jannovar.impl.parse.gtfgff.FeatureRecord.Strand
    • de.charite.compbio.jannovar.pedigree.Genotype
    • de.charite.compbio.jannovar.pedigree.Disease
    • de.charite.compbio.jannovar.pedigree.Sex
    • de.charite.compbio.jannovar.annotation.VariantEffect
    • de.charite.compbio.jannovar.annotation.OldVariantType
    • de.charite.compbio.jannovar.annotation.PutativeImpact
    • de.charite.compbio.jannovar.annotation.AnnotationMessage
    • de.charite.compbio.jannovar.annotation.AnnotationLocation.RankType
    • de.charite.compbio.jannovar.reference.Strand
    • de.charite.compbio.jannovar.reference.GenomeVariantType
    • de.charite.compbio.jannovar.reference.PositionType
    • de.charite.compbio.jannovar.hgnc.AltGeneIDType